As noon struck on Wednesday, Altaf Hussein Bhatt, the presiding officer for poll booth 18 in the old city of Srinagar smiled, shrugged and stated the obvious. "It is not very busy," he said.

Outside, in the dusty streets of Kashmir's summer capital, there were many heavily armed police officers and members of the paramilitaries – but few voters. Only 25 of the 747 local residents registered at booth 18, set up in a classroom of a local college, had cast their ballot. A long tedious afternoon loomed for Bhatt and his team.

Farooq Abdullah, the incumbent member of parliament for Srinagar, had voted earlier with his son, daughter and son-in-law at a booth on the other side of the city. Collectively, the family's visit had increased the turn out at polling station by a third.

"The vote is going very well. I feel good," Abdullah told the Guardian.

But the contrast with scenes elsewhere across India – where about 100 million people voted amid customary colour, crowds and chaos in the latest phase of the six-week long election – was striking. Turnout in the rest of the country has generally been high, sometimes 70 percent or more. But when the polls closed in Srinagar, only a quarter of its 1.2 million eligible voters had cast their ballots. By nightfall, a 17-year-old, wounded during running clashes between protestors and police during the afternoon, had died.

The violence underlined the special status of Kashmir, where decades of conflict have left layers of scars some fear may be reopened in coming months if – as widely predicted – the Hindu nationalist Bharatiya Janata party (BJP) form a government when national results are announced in 15 days time.

Time is now running out for Rahul Gandhi, the scion of India's foremost political dynasty and the face of the campaign of the Congress party, to counter the momentum generated by Narendra Modi, the chief minister of Gujarat state and the BJP prime ministerial candidate. Modi's promise to bring honest government, efficient services and renewed economic growth has struck a chord with voters tired of endemic corruption, intractable bureaucracy and rising prices.

But critics accuse the 63-year-old of sectarian prejudice and failing to stop, or even encouraging, mob violence in Gujarat in 2002 which left more than 1,000 people, largely Muslims, dead. He denies the claims but for many Kashmiris the prospect of his premiership raises deep concerns.

India's only Muslim majority state has been disputed by Pakistan and India since the two won independence from Britain in 1947. For the last 25 years, tens of thousands have died here as separatists and Islamic extremists have battled Indian national security forces and local police. Even if violence has ebbed in recent years, demands for autonomy or even independence remain strong. "Kashmir has become significant because the BJP is in the ascendant," said Samir Saran of the Observer Research Foundation, a Delhi-based thinktank .

One indicator of the relative strength of local militants and separatists, who have called for a boycott of the polls, is the turnout, in particular Srinagar. Separatist leaders said the boycott was justified by the heavy security presence in Kashmir.

"Voting is the soul of any democratic process but when cultural, social, political and religious rights are being trampled under the boots of 600,000 security personnel then elections mean nothing," said Mirwaiz Umer Farooq, head of the Awami Action Committee.

But Gul Mohammed Wani, professor of political science at Kashmir University, attributed the low turnout to disappointment with local government's ability to provide jobs and services, the lack of any progress in the peace process and a "fear psychosis" created by a series of shootings and grenade attacks blamed on militants in recent weeks. "Kashmir will turn out to be important [under a BJP government] because politically it remains very unstable," he said.

The BJP has a negligible presence in Srinagar and surrounding areas and, though they fielded candidates, were not expected to receive much support. Dynasty plays its role at local level as for the nation as a whole. The Abdullah family have dominated Kashmiri politics for decades, and their party has won the Srinagar seat in nine of the past 11 elections.

One key local concern is the prospect that a BJP government might implement a manifesto pledge and move to end the constitutional provisions which grant a degree of autonomy to Kashmir and special legal privileges to the country's Muslim population. This, said Farooq, could increase the risk of a return to widespread violence.

Modi's campaign rhetoric in recent weeks has also worried many. Though he has consistently promised "development for all", the he pledged to deport Muslim refugees from Bangladesh at a rally last weekend and an aide called on Hindu communities to take revenge through the ballot box for deaths in recent communal violence – which has spiked across India in the last ten months. A handful of Hindu extremists have gone further and, though disowned by Modi and his party, appear emboldened by his predicted success.

Senior BJP officials regularly accuse the Congress party of a "false secularism" and favouritism towards India's 150 million Muslims. "The BJP is a nationalist party and one of the key elements of that nationalism is an idea of 'India First' which means no exceptions for specific communities. One of the BJP's demands ever since its foundation [in 1980] has been no special treatment for Kashmir," said Saran. This, he added, ran counter to the idea that India was a "clever composition of rules that have given something to everyone if not everything to everyone".

But most voters in and around Srinagar said they were more concerned with local issues such as roads, clinics, schools and jobs than broader principles.

"We want a safe government which will help poor people like us," said Sunana Kaul, a school teacher whose father disappeared five years ago – one of the thousands of missing left by the conflict. Many spoke of their distrust of all politicians.

But 70-year-old Ghulam Qadir, who has voted in every election in Srinagar for more than four decades, was adamant that his duty was to "chose a government".

"Anyone who tells you not to vote is just jealous because they are not in power," he said, before walking carefully and slowly into polling booth 18 to become the 26th voter of the day.